[AMBER] PySander availability in PyTraj

From: David Poole <thepoole.ucdavis.edu>
Date: Sun, 3 Apr 2022 02:52:10 +0200

Hello Jason,

I realized that I could also put this problem up on the github for pytraj,
https://github.com/Amber-MD/pytraj/issues/1605 , but I will also put the
two examples here since this is closer to pysander people (perhaps):

We can construct an options set for PB using gas_input as a starting point;
then use an example trajectory to execute pbsa:

> options = sander.gas_input(8)
> options.igb = 0
> options.ipb = 2

fn, tn = get_fn('ala3')
> traj = pt.Trajectory(fn, tn)

 first=pt.esander(traj=traj, mm_options=options)
> second=pt.esander(traj=traj, mm_options=options)


Alternatively, you can just specify igb=10; which also works:

> fn, tn = get_fn('ala3')
> traj = pt.Trajectory(fn, tn)
> first=pt.esander(traj=traj, igb=10)
> second=pt.esander(traj=traj, igb=10)


These are both setup to use pytraj/pysander.

Hope this shines some light on it,
~David

Hi David,


> I don't think I've ever tried the PB interface through the sander API. Do
> you have an example script that shows the error you're seeing?


> Thanks,
> Jason
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 02 2022 - 18:00:02 PDT
Custom Search